I'm using openfire 3.9.3 with debian 7 and I can only start openfire over the setup routine. If I stop openfire and start it again with "service openfire start" nothing happens. I first have to change in the openfire.xml the line "<setup>true</setup>" to false. Then I can run through the setup and everything works fine.
I didn't find another post that has the same problem. Maybe someone can help me.